Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations

Tom K. Woo, Luigi Cavallo, Tom Ziegler*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

159 Scopus citations

Abstract

A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras and Morokuma that is used to perform combined quantum mechanics/ molecular mechanics (QM/MM) molecular dynamics simulations, frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system, thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM frequency calculations.

Original languageEnglish (US)
Pages (from-to)307-313
Number of pages7
JournalTheoretical Chemistry Accounts
Volume100
Issue number5-6
DOIs
StatePublished - Dec 11 1998

Keywords

  • Frequencies
  • Macromolecular systems
  • Molecular dynamics
  • Molecular mechanics
  • Quantum mechanics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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